Noncanonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only ten nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols u...

Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins in...

MOTIVATION Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs. However, these motifs are often difficult to identify owing to their high divergence. The motif structure included explicitly into the motif recognition algorithm improves recognition efficiency f...

Most biological actions of proteins depend on some typical parts of their three-dimensional structure, called 3D motifs. To automatically discover corresponding 3D motifs between proteins, we propose a new 3D substructure matching algorithm based on geometric hashing techniques. The key feature of the method is the introduction of a 3D reference frame attached to each amino acid. This allows to...

Coiled coils are important protein-protein interaction motifs with high specificity that are used to assemble macromolecular complexes. Their simple geometric organization, consisting of alpha helices wrapped around each other, confers remarkable mechanical properties. A geometrical and mechanical continuous model taking into account sequence effects and based on the superhelical winding of the...

(received 4 jan 2014, accepted 2 mar 2014) abstract mazandaran, the northern province of iran, as an area with a different climate and political situation in their own special place has been allocated with itself in the history of this land. researchers familiar with the history, culture and art of ancient civilizations, have known this place a good platform for own exploring and searching. the...

background: computational identification of phylogenetic motifs helps to understand the knowledge about known functional features that includes catalytic site, substrate binding epitopes, and protein-protein interfaces. furthermore, they are strongly conserved among orthologs, indicating their evolutionary importance. the study aimed to analyze five candidate genes involved in type ii diabetic ...

The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for th...